[English] 日本語
Yorodumi
- PDB-6h5f: LtgA disordered Helix -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h5f
TitleLtgA disordered Helix
ComponentsPutative soluble lytic murein transglycosylase
KeywordsTRANSFERASE / Peptidoglycan / antibiotic resistance / enzyme hub
Function / homology
Function and homology information


catalytic activity / hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space / metal ion binding
Similarity search - Function
Lytic transglycosylase, superhelical linker domain superfamily / Lytic transglycosylase, superhelical U-shaped / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Soluble lytic murein transglycosylase
Similarity search - Component
Biological speciesNeisseria meningitidis NM422 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWilliams, A.H.
CitationJournal: Elife / Year: 2020
Title: Defective lytic transglycosylase disrupts cell morphogenesis by hindering cell wall de-O-acetylation inNeisseria meningitidis.
Authors: Williams, A.H. / Wheeler, R. / Deghmane, A.E. / Santecchia, I. / Schaub, R.E. / Hicham, S. / Moya Nilges, M. / Malosse, C. / Chamot-Rooke, J. / Haouz, A. / Dillard, J.P. / Robins, W.P. / ...Authors: Williams, A.H. / Wheeler, R. / Deghmane, A.E. / Santecchia, I. / Schaub, R.E. / Hicham, S. / Moya Nilges, M. / Malosse, C. / Chamot-Rooke, J. / Haouz, A. / Dillard, J.P. / Robins, W.P. / Taha, M.K. / Gomperts Boneca, I.
History
DepositionJul 24, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionAug 28, 2019ID: 4YP4
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative soluble lytic murein transglycosylase


Theoretical massNumber of molelcules
Total (without water)67,8241
Polymers67,8241
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.822, 72.256, 122.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Putative soluble lytic murein transglycosylase


Mass: 67824.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis NM422 (bacteria)
Gene: NMB1949 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: Q9JXP1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.38 % / Description: RECTANGULAR IN SHAPE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 33% (W/V) PEG 6000, 0.01 M TRI SODIUM CITRATE., PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.955→49.06 Å / Num. obs: 40499 / % possible obs: 98.6 % / Redundancy: 7.74 % / Rsym value: 0.055 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 1.47 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YIB

4yib
PDB Unreleased entry


Resolution: 2→49.06 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.97
RfactorNum. reflection% reflection
Rfree0.246 1999 4.94 %
Rwork0.193 --
obs0.196 40497 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 0 271 4651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074478
X-RAY DIFFRACTIONf_angle_d0.9636065
X-RAY DIFFRACTIONf_dihedral_angle_d14.2421655
X-RAY DIFFRACTIONf_chiral_restr0.038645
X-RAY DIFFRACTIONf_plane_restr0.004807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9952-2.04510.35821100.32742564X-RAY DIFFRACTION92
2.0451-2.10040.35411570.29472674X-RAY DIFFRACTION98
2.1004-2.16220.30251390.27022702X-RAY DIFFRACTION98
2.1622-2.2320.29071340.23952715X-RAY DIFFRACTION99
2.232-2.31180.30511490.21542691X-RAY DIFFRACTION98
2.3118-2.40440.29321400.21742752X-RAY DIFFRACTION99
2.4044-2.51380.29241360.21622720X-RAY DIFFRACTION99
2.5138-2.64630.28731450.21782749X-RAY DIFFRACTION99
2.6463-2.81210.26461410.22162764X-RAY DIFFRACTION99
2.8121-3.02920.34231570.22892762X-RAY DIFFRACTION99
3.0292-3.3340.28711430.21122785X-RAY DIFFRACTION100
3.334-3.81620.22281470.18122810X-RAY DIFFRACTION100
3.8162-4.80740.22031480.15142836X-RAY DIFFRACTION100
4.8074-49.07380.18861530.16672974X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more